In each of the 16 academic departments of the University of Crete, there is a Doctoral Studies Program with research, innovation and connection to the labor market. Each interested candidate submits an application for the preparation of a doctoral thesis to the Department's Secretariat, accompanied by the relevant research proposal and the other required supporting documents specified in the Doctoral Studies Regulations of each Department.

By decision of the Department's Assembly, PhD candidates are accepted, a three-member advisory committee is appointed to supervise and guide them.

The duration of time for obtaining the doctoral degree cannot be less than three (3) calendar years from the date of appointment of the three-member advisory committee.

In the context of extroversion and the promotion of knowledge, Special Cooperation Protocols have been concluded with recognized Institutions abroad for the preparation of a doctoral thesis with co-supervision.